A method for determining whether to modify a manufacturing process recipe is provided. A substrate to be processed at a manufacturing system according to the first process recipe is identified. An instruction to transfer the substrate to a substrate measurement subsystem to obtain a first set of measurements for the substrate is generated. The first set of measurements for the substrate is received from the substrate measurement subsystem. An instruction to transfer the substrate from the substrate measurement subsystem to a processing chamber is generated. A second set of measurements for the substrate is received from one or more sensors of the processing chamber. A first mapping between the first set of measurements and the second set of measurements for the substrate is generated. The first set of measurements mapped to the second set of measurements for the substrate is stored. A determination is made based on the first set of measurements mapped to the second set of measurements for the substrate of whether to modify the first process recipe or a second process recipe for the substrate.